Mega Man's the one with the strong sense of justice. Roll thinks they got just what the deserved. Besides it's not like letting them tough it out in a cell goes against any of the three laws of robotics. Except maybe the one about following all orders given by a humans. But I'm sure Dr. Light must have told her not to do what the Two Evil Scientists say so it all works out.

Sometimes sacrifices must be made to ensure safety. Look @ I Robot, all those robots had the 3 Laws, and they still held humans against their will because they were a danger to themselves. And the main CPU said some human deaths were necessary to keep that protection.